Wednesday's no-confidence motion was brought against Giacomo Caliendo, a junior justice minister.
Caliendo, who has denied all wrongdoing, is currently under investigation, accused of belonging to a secret group that tried to influence the appointments of judges.
The vote, which failed by 70 votes, was parliament's last politically significant act until September as it goes into its summer recess.
Fini's supporters sided with a group of centrist and moderate deputies, bringing the number of abstentions to 75 and proving that they could have cost the government its majority.
Giovanni Orsina, a political science professor at Rome's LUISS university, said that abstaining "is quite enough to signal that this is a major problem in Berlusconi's majority".
"What is going to happen next is very difficult to foretell. Maybe they will still find a way to work together," he said
"Or maybe their roads are going to get more and more separated, and this means that there is a possibility ... of an early dissolution of parliament and elections."
Defending the prime minister following the vote, Umberto Bossi, leader of the Northern League party and Berlusconi's staunchest partner in the coalition, said: "This is a signal that we're staying on and that there is no election now."
Berlusconi's spectacular split with Fini has been played out with venomous accusations on both sides.
Fini had been an ally since Berlusconi's entry into politics 16 years ago and is the co-founder of the ruling People of Freedom party.
The two had bickered for months on a number of issues, most notably morality in politics in the wake of scandals hitting coalition members.
Fini has taken a harsher stance than Berlusconi, demanding that public officials suspected of corruption resign.
Last week, Berlusconi accused Fini of mounting an opposition from within and working against the government, effectively expelling him from the party.
Fini, who said Berlusconi behaved more like a manager than a premier, then split from the coalition and created his own faction, called the Freedom and Future for Italy.
For all his acrimonious words, Fini says his politicians will support the government when it carries out the joint electoral platform under which the coalition was voted into power in 2008.
But he says they will oppose it when they consider its policies unjust or against the common good.
Berlusconi has issued reassurances that his government is stable.
However, in recent days he has also warned that he will push for early elections at the first sign of trouble.
The government's term is due to end in 2013.